DOCSLIB.ORG

TITLE PAGE Upload This Completed Form to Website with Submission

Total Page：16

File Type：pdf, Size：1020Kb

Download full-text PDF Read full-text
TITLE PAGE Upload This Completed Form to Website with Submission JAST (Journal of Animal Science and Technology) TITLE PAGE Upload this completed form to website with submission ARTICLE INFORMATION Fill in information in each box below Article Type Research article Article Title (within 20 words without abbreviations) Complete genome sequence of Paenibacillus konkukensis sp. nov. SK3146 as a potential probiotic strain Running Title (within 10 words) Complete genome sequence of Paenibacillus konkukensis sp. nov. SK3146 Author Hae-In Jung1, Sungkwon Park2, Kai-Min Niu3, Sang-Won Lee4, Damini Kothari1, Kwon Jung Yi1, and Soo-Ki Kim1 Affiliation 1 Department of Animal Sciences and Technology, Konkuk University, Seoul 05029, Korea 2 Department of Food Science and Biotechnology, Sejong University, Seoul 05005, Korea 3 Institute of Biological Resources, Jiangxi Academy of Sciences, Nanchang 330029, China 4 College of Veterinary Medicine, Konkuk University, Seoul 05029, Korea ORCID (for more information, please visit Hae-In Jung (https://orcid.org/ 0000-0003-2643-6681) https://orcid.org) Sungkwon Park(https://orcid.org/0000-0002-7684-9719) Kai-Min Niu (https://orcid.org/0000-0002-9756-3517) Sang-Won Lee (https://orcid.org/0000-0003-1956-7245) Damini Kothari (https://orcid.org/0000-0003-3627-2377) Kwon Jung Yi (https://orcid.org/0000-0001-6002-0378) Soo-Ki Kim (https://orcid.org/ 0000-0003-3499-3330) Competing interests No potential conflict of interest relevant to this article was reported. Funding sources Not applicable. State funding sources (grants, funding sources, equipment, and supplies). Include name and number of grant if available. Acknowledgements This research was supported by a grant from Agricultural Science and Technology Development Program (Project No. PJ010906), Rural Development Administration, Republic of Korea. Availability of data and material Upon reasonable request, the datasets of this study can be available from the corresponding author. Authors' contributions Conceptualization: Jung HI, Lee SW, Park SK, Kim SK. Please specify the authors’ role using this form. Data curation: Jung HI. Formal analysis: Jung HI, Niu KM ACCETEDMethodology: Jung HI. Validation: Jung HI, Lee SW Investigation: Jung HI. Yi KJ Writing - original draft: Jung HI, Lee SW Writing - review & editing: Niu KM, Lee SW, Park SK, Kim SK. Ethics approval and consent to participate This article does not require IRB/IACUC approval because there are no human and animal participants. CORRESPONDING AUTHOR CONTACT INFORMATION For the corresponding author (responsible for Fill in information in each box below correspondence, proofreading, and reprints) First name, middle initial, last name Soo-Ki Kim Email address – this is where your proofs will be sent [email protected] Secondary Email address [email protected] Address Department of Animal Sciences and Technology, Konkuk University, Seoul 05029, Korea. Cell phone number +82-10-2965-3728 Office phone number +82-2-450-3728 Fax number +82-2-458-3728 ACCETED Abstract Paenibacillus konkukensis sp. nov., SK3146 is a novel strain isolated from a pig feed. Here, we present complete genome sequence of SK3146. The genome consists of a single circular genome measuring 7,968,964 bp in size with an average G+C content of 53.4%. Genomic annotation revealed that the strain encodes 151 proteins related to hydrolases (EC3), which was higher than those in Bacillus subtilis and Escherichia coli. Diverse kinds of hydrolases including galactosidase, glucosidase, cellulase, lipase, xylanase, and protease were found in the genome of SK3146, coupled with one bacteriocin encoding gene. The complete genome sequence of P. konkukensis SK3146 indicates the immense probiotic potential of the strain with nutrient digestibility and antimicrobial activity functions. Keywords: Paenibacillus, Complete genome sequence, Exoenzyme, Feed additive ACCETED The well-being and health status of economic animals are more deteriorative due to the intensive farming practices. Feed-additives probiotics including lactic acid bacteria and Bacillus spp. are commonly used to modulate host health and improve performance in pig production [1, 2]. Typically, a culture-dependent isolation coupled with in-vitro characterization methods have been used to establish probiotic potential of the strains. Due to rapid development of next generation sequencing in the past decade, scientists are now exploring whole genome sequencing to identify and functionally characterize novel probiotic strains. A number of potential probiotic strains have been identified based on their putative functional genes from their whole genome [3]. Paenibacillus spp. are well known as growth promoters for crops, but there are very limited studies exploring their probiotic potentials, despite the fact that they can produce diverse kinds of active substances namely antimicrobial peptides (bacteriocin and lipopeptide), volatile organic compounds, and digestive enzymes (amylase, cellulase, lipase, protease, etc), among many others [4]. Previously, we have isolated a novel Paenibacillus strain SK3146T (=KACC 18876T=LMG 29568T) from a pig feed, which was taxonomically assigned as Paenibacillus konkukensis sp. nov. [5]. In this study, we provide a detailed description of the complete genome sequence of SK3146 and analyzed its putative functional genes related to digestive enzymes and bacteriocin which could be beneficial attributes as a functional feed additive. SK3146 was cultured in Luria-Bertani broth for two days at 37℃ under shaking conditions (100 rpm). Genomic DNA of SK3146ACCETED was extracted using the Wizard Genomic DNA Purification Kit (Promega Corporation, Madison, WI, USA) according to the manufacturer’s instructions. The genome of SK3146 was completely sequenced using the PacBio® RS II system by Macrogen Inc. (Seoul, South Korea). The PacBio RS II system libraries were prepared using the SMRTbell template prep kit v 1.0. In total, 142,242 bp PacBio subreads with 1,041,901,553 bp were generated using the PacBio® RS II system, and their meal length and N50 value were 7,324 and 10,697 bp, respectively. The sequencing reads were de novo assembled using the HGAP analysis with default options. The assembly was completed with the PacBio RS II system. Annotation of coding DNA sequence (CDS) and functional genes were analyzed by the Prokka v1.10. The general features of the SK3146 were analyzed based on its complete genome sequence using the Geneious 8.1.9 software (Biomatters, New Zealand) [6]. The predicted CDS were classified depending on the clusters of orthologous genes (COG), followed by the construction of a circular genome map and analysis of protein function by a web server: Bacterial Annotation System (https://www.basys.ca/) [7]. The circular genome visualization and general features of SK3146 genome are presented in Fig. 1 and summarized in Table 1, respectively. The complete genome of the strain consists of a single circular chromosome measuring 7,968,964 bp in size and 53.4% in G+C content. A total of 6,988 genes were predicted in the genome including 6,842 CDS, 37 ribosomal RNAs (rRNA), 108 transfer RNAs (tRNA), and 1 transfer-messenger RNA (tmRNA) loci. In addition, 10 CRISPR elements, three prophage regions, and 16 IS elements were identified in the genome. Furthermore, we have analyzed the presence of potential enzymes in the genome of SK3146 via protein function annotation with the Kyoto Encyclopedia of Genes and Genomes database, which provide specific substrates, reactions, and enzyme nomenclature [8]. We then categorized the genes encoding potential enzymes of SK3146 according to enzyme code number. The class of hydrolases (EC3) including galactosidase, glucosidase, cellulase, lipase, xylanase, protease, and others in SK3146 are listed in Table 2. EC3 hydrolases including phosphatases, glycosidases, peptidases, nucleosidases, and lipases are widely used in feed additive industry to improve digestibility and bioavailability of nutrients in animal feeds [9]. Besides enzyme encoding genes, one bacteriocin encoding gene was also foundACCETED on the chromosome of SK3146. The hydrolytic enzymes such as glucanase, cellulase, protease, and chitinase of Paenibacillus have been reported to have anti-fungal activities via destruction of fungal cell wall [10]. Moreover, β-glucosidase, cellulase, xylanase, and protease have been demonstrated to reduce carbohydrate- and protein-based anti-nutritional factors present in the plant-derived protein sources and consequently improving the nutritional quality of feed [11]. In the present study, the complete genome of P. konkukensis sp. nov., SK3146 isolated from a pig feed has been reported. The genome of SK3146 encodes multiple enzymes that could be applied to improve the digestibility and bioavailability of nutrients of animal feed. A gene encoding bacteriocin was also identified. Thus, the genome mining conducted in this study suggests that stain SK3146 has significant potential as a probiotic for use in feed additive applications. In addition, the genome information of SK3146 widens our understanding on the whole genus of Paenibacillus to explore and develop next generation probiotics. The genome-based protein prediction will be validated by in vitro characterization and in vivo animal study in near future. Genomic sequence accession number The complete genome sequence of P. konkukensis sp. nov., SK3146 was deposited in the GenBank under the accession number CP027059. ACCETED References 1. Barba-Vidal E, Martin-Orue SM, Castillejos L. Practical aspects of the use of probiotics in pig
Load more

Recommended publications
  • WO 2007/084545 Al
    (12) INTERNATIONAL APPLICATION PUBLISHED UNDER THE PATENT COOPERATION TREATY (PCT) (19) World Intellectual Property Organization International Bureau (43) International Publication Date (10) International Publication Number 26 July 2007 (26.07.2007) PCT WO 2007/084545 Al (51) International Patent Classification: (74) Agent: ZERULL, Susan, Moeller; The Dow Chemical C07C 227/32 (2006.01) C12P 41/00 (2006.01) Company, Intellectual Property Section, P.O. Box 1967, C07D 317/30 (2006.01) Midland, MI 48674-1967 (US). (21) International Application Number: (81) Designated States (unless otherwise indicated, for every PCT/US2007/001207 kind of national protection available): AE, AG, AL, AM, AT,AU, AZ, BA, BB, BG, BR, BW, BY, BZ, CA, CH, CN, (22) International Filing Date: 17 January 2007 (17.01.2007) CO, CR, CU, CZ, DE, DK, DM, DZ, EC, EE, EG, ES, FI, (25) Filing Language: English GB, GD, GE, GH, GM, GT, HN, HR, HU, ID, IL, IN, IS, JP, KE, KG, KM, KN, KP, KR, KZ, LA, LC, LK, LR, LS, (26) Publication Language: English LT, LU, LV,LY,MA, MD, MG, MK, MN, MW, MX, MY, (30) Priority Data: MZ, NA, NG, NI, NO, NZ, OM, PG, PH, PL, PT, RO, RS, 11/333,937 18 January 2006 (18.01.2006) US RU, SC, SD, SE, SG, SK, SL, SM, SV, SY, TJ, TM, TN, (71) Applicant (for all designated States except US): DOW TR, TT, TZ, UA, UG, US, UZ, VC, VN, ZA, ZM, ZW GLOBAL TECHNOLOGIES INC. [US/US]; Washing (84) Designated States (unless otherwise indicated, for every ton Street, 1790 Building, Midland, MI 48674 (US).
    [Show full text]
  • HEAT INACTIVATION of THIAMINASE in WHOLE FISH by R
    August 1966 COMMERCIAL FISHERIES REVIEW 11 HEAT INACTIVATION OF THIAMINASE IN WHOLE FISH By R. H. Gnaedinger and R. A. Krzeczkowskil,c ABSTRACT The time required at various temperatures to inactivate all of the thiam inase in several species of whole fish was studied. Some effects of pH and enzyme concentra ­ tion on the time-temperature inactivation were also determined. Whole raw fish were ground! sealed in spec~ally-constructed m etal cans, heated a t various tempera ­ tures .for. varIOUS length.s <;>f tune! and analyzed for residual thiaminase a ct ivity. Re ­ sul~ md.lcate that a m~un .um tune -tempe.rature of 5 minutes a t 1800 F. is required t<;> mac.tlvate all the .thl~mma s e of who.le hsh. Enzyme concentrations, pH, a nd pos­ slbly 011 c ontent of flsh mfluence the tune required to destroy thiaminase. INTRODUCTION The heating conditions employed b y commercial mink-food producers and mink ranchers ;0 destroy thiaminase in whole fish are empiri cal. The conditions are not based on predeter­ nined time-temperature relations for the thermal inactivation of this antimetabolite. A com­ mon practice, for example, is to cook the fish at 1800 -2000 F. for 15 minutes (Bor gstrom 1962). Most of the specific data available on the time -temperature r e la tion is found in various research publications dealing with the occurrence of thiamina s e in fish , or with studies on the chemistry of the enzyme. Deutsch and Hasler (1943) used 15 m i nutes at 100 0 C .
    [Show full text]
  • Control Engineering Perspective on Genome-Scale Metabolic Modeling
    Control Engineering Perspective on Genome-Scale Metabolic Modeling by Andrew Louis Damiani A dissertation submitted to the Graduate Faculty of Auburn University in partial fulfillment of the requirements for the Degree of Doctor of Philosophy Auburn, Alabama December 12, 2015 Key words: Scheffersomyces stipitis, Flux Balance Analysis, Genome-scale metabolic models, System Identification Framework, Model Validation, Phenotype Phase Plane Analysis Copyright 2015 by Andrew Damiani Approved by Jin Wang, Chair, Associate Professor of Chemical Engineering Q. Peter He, Associate Professor of Chemical Engineering, Tuskegee University Thomas W. Jeffries, Professor of Bacteriology, Emeritus; University of Wisconsin-Madison Allan E. David, Assistant Professor of Chemical Engineering Yoon Y. Lee, Professor of Chemical Engineering Abstract Fossil fuels impart major problems on the global economy and have detrimental effects to the environment, which has caused a world-wide initiative of producing renewable fuels. Lignocellulosic bioethanol for renewable energy has recently gained attention, because it can overcome the limitations that first generation biofuels impose. Nonetheless, in order to have this process commercialized, the biological conversion of pentose sugars, mainly xylose, needs to be improved. Scheffersomyces stipitis has a physiology that makes it a valuable candidate for lignocellulosic bioethanol production, and lately has provided genes for designing recombinant Saccharomyces cerevisiae. In this study, a system biology approach was taken to understand the relationship of the genotype to phenotype, whereby genome-scale metabolic models (GSMMs) are used in conjunction with constraint-based modeling. The major restriction of GSMMs is having an accurate methodology for validation and evaluation. This is due to the size and complexity of the models.
    [Show full text]
  • Generated by SRI International Pathway Tools Version 25.0, Authors S
    An online version of this diagram is available at BioCyc.org. Biosynthetic pathways are positioned in the left of the cytoplasm, degradative pathways on the right, and reactions not assigned to any pathway are in the far right of the cytoplasm. Transporters and membrane proteins are shown on the membrane. Periplasmic (where appropriate) and extracellular reactions and proteins may also be shown. Pathways are colored according to their cellular function. Gcf_000238675-HmpCyc: Bacillus smithii 7_3_47FAA Cellular Overview Connections between pathways are omitted for legibility.
    [Show full text]
  • 1 Metabolic Dysfunction Is Restricted to the Sciatic Nerve in Experimental
    Page 1 of 255 Diabetes Metabolic dysfunction is restricted to the sciatic nerve in experimental diabetic neuropathy Oliver J. Freeman1,2, Richard D. Unwin2,3, Andrew W. Dowsey2,3, Paul Begley2,3, Sumia Ali1, Katherine A. Hollywood2,3, Nitin Rustogi2,3, Rasmus S. Petersen1, Warwick B. Dunn2,3†, Garth J.S. Cooper2,3,4,5* & Natalie J. Gardiner1* 1 Faculty of Life Sciences, University of Manchester, UK 2 Centre for Advanced Discovery and Experimental Therapeutics (CADET), Central Manchester University Hospitals NHS Foundation Trust, Manchester Academic Health Sciences Centre, Manchester, UK 3 Centre for Endocrinology and Diabetes, Institute of Human Development, Faculty of Medical and Human Sciences, University of Manchester, UK 4 School of Biological Sciences, University of Auckland, New Zealand 5 Department of Pharmacology, Medical Sciences Division, University of Oxford, UK † Present address: School of Biosciences, University of Birmingham, UK *Joint corresponding authors: Natalie J. Gardiner and Garth J.S. Cooper Email: [email protected]; [email protected] Address: University of Manchester, AV Hill Building, Oxford Road, Manchester, M13 9PT, United Kingdom Telephone: +44 161 275 5768; +44 161 701 0240 Word count: 4,490 Number of tables: 1, Number of figures: 6 Running title: Metabolic dysfunction in diabetic neuropathy 1 Diabetes Publish Ahead of Print, published online October 15, 2015 Diabetes Page 2 of 255 Abstract High glucose levels in the peripheral nervous system (PNS) have been implicated in the pathogenesis of diabetic neuropathy (DN). However our understanding of the molecular mechanisms which cause the marked distal pathology is incomplete. Here we performed a comprehensive, system-wide analysis of the PNS of a rodent model of DN.
    [Show full text]
  • Effects of Dietary Thiaminase on Reproductive Traits in Three Populations of Atlantic Salmon Targeted for Reintroduction Into Lake Ontario
    Western University Scholarship@Western Electronic Thesis and Dissertation Repository 1-22-2020 1:00 PM Effects of dietary thiaminase on reproductive traits in three populations of Atlantic salmon targeted for reintroduction into Lake Ontario Kimberly T. Mitchell The University of Western Ontario Supervisor Neff, Bryan D. The University of Western Ontario Graduate Program in Biology A thesis submitted in partial fulfillment of the equirr ements for the degree in Master of Science © Kimberly T. Mitchell 2020 Follow this and additional works at: https://ir.lib.uwo.ca/etd Part of the Aquaculture and Fisheries Commons, Biodiversity Commons, and the Terrestrial and Aquatic Ecology Commons Recommended Citation Mitchell, Kimberly T., "Effects of dietary thiaminase on reproductive traits in three populations of Atlantic salmon targeted for reintroduction into Lake Ontario" (2020). Electronic Thesis and Dissertation Repository. 6826. https://ir.lib.uwo.ca/etd/6826 This Dissertation/Thesis is brought to you for free and open access by Scholarship@Western. It has been accepted for inclusion in Electronic Thesis and Dissertation Repository by an authorized administrator of Scholarship@Western. For more information, please contact [email protected]. Abstract The fitness of reintroduced salmonids in Lake Ontario can be reduced by high levels of thiaminase in exotic prey consumed at the adult stage. If sensitivity to dietary thiaminase differs among the three Atlantic salmon populations targeted for reintroduction into Lake Ontario, this could significantly influence their performance. I quantified the effects of experimental diets that contained high or low (control) levels of thiaminase on thiamine concentrations, survival, growth rate, and reproductive traits (sperm and egg quality) in Atlantic salmon from the three candidate source populations.
    [Show full text]
  • Yeast Genome Gazetteer P35-65
    gazetteer Metabolism 35 tRNA modification mitochondrial transport amino-acid metabolism other tRNA-transcription activities vesicular transport (Golgi network, etc.) nitrogen and sulphur metabolism mRNA synthesis peroxisomal transport nucleotide metabolism mRNA processing (splicing) vacuolar transport phosphate metabolism mRNA processing (5’-end, 3’-end processing extracellular transport carbohydrate metabolism and mRNA degradation) cellular import lipid, fatty-acid and sterol metabolism other mRNA-transcription activities other intracellular-transport activities biosynthesis of vitamins, cofactors and RNA transport prosthetic groups other transcription activities Cellular organization and biogenesis 54 ionic homeostasis organization and biogenesis of cell wall and Protein synthesis 48 plasma membrane Energy 40 ribosomal proteins organization and biogenesis of glycolysis translation (initiation,elongation and cytoskeleton gluconeogenesis termination) organization and biogenesis of endoplasmic pentose-phosphate pathway translational control reticulum and Golgi tricarboxylic-acid pathway tRNA synthetases organization and biogenesis of chromosome respiration other protein-synthesis activities structure fermentation mitochondrial organization and biogenesis metabolism of energy reserves (glycogen Protein destination 49 peroxisomal organization and biogenesis and trehalose) protein folding and stabilization endosomal organization and biogenesis other energy-generation activities protein targeting, sorting and translocation vacuolar and lysosomal
    [Show full text]
  • Nitrilase 1 Modulates Lung Tumor Progression in Vitro and in Vivo
    www.impactjournals.com/oncotarget/ Oncotarget, Vol. 7, No. 16 Nitrilase 1 modulates lung tumor progression in vitro and in vivo Yong Antican Wang1, Yunguang Sun2,5, Justin M. Le Blanc1, Charalambos Solomides3, Tingting Zhan4, Bo Lu1 1Department of Radiation Oncology, Thomas Jefferson University, Philadelphia, PA, 19107, USA 2Department of Cancer Biology, Thomas Jefferson University, Philadelphia, PA, 19107, USA 3Department of Pathology, Thomas Jefferson University, Philadelphia, PA, 19107, USA 4Department of Pharmacology, Thomas Jefferson University, Philadelphia, PA, 19107, USA 5Department of Pathology, Medical College of Wisconsin, Milwaukee, WI, 53226, USA Correspondence to: Bo Lu, e-mail: [email protected]. Keywords: NIT1, lung cancer, KRAS, NSCLC, tumor suppressor Received: October 01, 2015 Accepted: January 23, 2016 Published: March 10, 2016 ABSTRACT Uncovering novel growth modulators for non-small cell lung cancer (NSCLC) may lead to new therapies for these patients. Previous studies suggest Nit1 suppresses chemically induced carcinogenesis of the foregut in a mouse model. In this study we aimed to determine the role of Nit1 in a transgenic mouse lung cancer model driven by a G12D Kras mutation. Nit1 knockout mice (Nit1−/−) were crossed with KrasG12D/+ mice to investigate whether a G12D Kras mutation and Nit1 inactivation interact to promote or inhibit the development of NSCLC. We found that lung tumorigenesis was suppressed in the Nit1-null background (Nit1−/−:KrasG12D/+). Micro-CT scans and gross tumor measurements demonstrated a 5-fold reduction in total tumor volumes compared to Nit1+/+KrasG12D/+ (p<0.01). Furthermore, we found that Nit1 is highly expressed in human lung cancer tissues and cell lines and use of siRNA against Nit1 decreased overall cell survival of lung cancer cells in culture.
    [Show full text]
  • ASPA Gene Aspartoacylase
    ASPA gene aspartoacylase Normal Function The ASPA gene provides instructions for making an enzyme called aspartoacylase. In the brain, this enzyme breaks down a compound called N-acetyl-L-aspartic acid (NAA) into aspartic acid (an amino acid that is a building block of many proteins) and another molecule called acetic acid. The production and breakdown of NAA appears to be critical for maintaining the brain's white matter, which consists of nerve fibers surrounded by a myelin sheath. The myelin sheath is the covering that protects nerve fibers and promotes the efficient transmission of nerve impulses. The precise function of NAA is unclear. Researchers had suspected that it played a role in the production of the myelin sheath, but recent studies suggest that NAA does not have this function. The enzyme may instead be involved in the transport of water molecules out of nerve cells (neurons). Health Conditions Related to Genetic Changes Canavan disease More than 80 mutations in the ASPA gene are known to cause Canavan disease, which is a rare inherited disorder that affects brain development. Researchers have described two major forms of this condition: neonatal/infantile Canavan disease, which is the most common and most severe form, and mild/juvenile Canavan disease. The ASPA gene mutations that cause the neonatal/infantile form severely impair the activity of aspartoacylase, preventing the breakdown of NAA and allowing this substance to build up to high levels in the brain. The mutations that cause the mild/juvenile form have milder effects on the enzyme's activity, leading to less accumulation of NAA.
    [Show full text]
  • Supplementary Table S4. FGA Co-Expressed Gene List in LUAD
    Supplementary Table S4. FGA co-expressed gene list in LUAD tumors Symbol R Locus Description FGG 0.919 4q28 fibrinogen gamma chain FGL1 0.635 8p22 fibrinogen-like 1 SLC7A2 0.536 8p22 solute carrier family 7 (cationic amino acid transporter, y+ system), member 2 DUSP4 0.521 8p12-p11 dual specificity phosphatase 4 HAL 0.51 12q22-q24.1histidine ammonia-lyase PDE4D 0.499 5q12 phosphodiesterase 4D, cAMP-specific FURIN 0.497 15q26.1 furin (paired basic amino acid cleaving enzyme) CPS1 0.49 2q35 carbamoyl-phosphate synthase 1, mitochondrial TESC 0.478 12q24.22 tescalcin INHA 0.465 2q35 inhibin, alpha S100P 0.461 4p16 S100 calcium binding protein P VPS37A 0.447 8p22 vacuolar protein sorting 37 homolog A (S. cerevisiae) SLC16A14 0.447 2q36.3 solute carrier family 16, member 14 PPARGC1A 0.443 4p15.1 peroxisome proliferator-activated receptor gamma, coactivator 1 alpha SIK1 0.435 21q22.3 salt-inducible kinase 1 IRS2 0.434 13q34 insulin receptor substrate 2 RND1 0.433 12q12 Rho family GTPase 1 HGD 0.433 3q13.33 homogentisate 1,2-dioxygenase PTP4A1 0.432 6q12 protein tyrosine phosphatase type IVA, member 1 C8orf4 0.428 8p11.2 chromosome 8 open reading frame 4 DDC 0.427 7p12.2 dopa decarboxylase (aromatic L-amino acid decarboxylase) TACC2 0.427 10q26 transforming, acidic coiled-coil containing protein 2 MUC13 0.422 3q21.2 mucin 13, cell surface associated C5 0.412 9q33-q34 complement component 5 NR4A2 0.412 2q22-q23 nuclear receptor subfamily 4, group A, member 2 EYS 0.411 6q12 eyes shut homolog (Drosophila) GPX2 0.406 14q24.1 glutathione peroxidase
    [Show full text]
  • Open Matthew R Moreau Ph.D. Dissertation Finalfinal.Pdf
    The Pennsylvania State University The Graduate School Department of Veterinary and Biomedical Sciences Pathobiology Program PATHOGENOMICS AND SOURCE DYNAMICS OF SALMONELLA ENTERICA SEROVAR ENTERITIDIS A Dissertation in Pathobiology by Matthew Raymond Moreau 2015 Matthew R. Moreau Submitted in Partial Fulfillment of the Requirements for the Degree of Doctor of Philosophy May 2015 The Dissertation of Matthew R. Moreau was reviewed and approved* by the following: Subhashinie Kariyawasam Associate Professor, Veterinary and Biomedical Sciences Dissertation Adviser Co-Chair of Committee Bhushan M. Jayarao Professor, Veterinary and Biomedical Sciences Dissertation Adviser Co-Chair of Committee Mary J. Kennett Professor, Veterinary and Biomedical Sciences Vijay Kumar Assistant Professor, Department of Nutritional Sciences Anthony Schmitt Associate Professor, Veterinary and Biomedical Sciences Head of the Pathobiology Graduate Program *Signatures are on file in the Graduate School iii ABSTRACT Salmonella enterica serovar Enteritidis (SE) is one of the most frequent common causes of morbidity and mortality in humans due to consumption of contaminated eggs and egg products. The association between egg contamination and foodborne outbreaks of SE suggests egg derived SE might be more adept to cause human illness than SE from other sources. Therefore, there is a need to understand the molecular mechanisms underlying the ability of egg- derived SE to colonize the chicken intestinal and reproductive tracts and cause disease in the human host. To this end, the present study was carried out in three objectives. The first objective was to sequence two egg-derived SE isolates belonging to the PFGE type JEGX01.0004 to identify the genes that might be involved in SE colonization and/or pathogenesis.
    [Show full text]
  • Structures, Functions, and Mechanisms of Filament Forming Enzymes: a Renaissance of Enzyme Filamentation
    Structures, Functions, and Mechanisms of Filament Forming Enzymes: A Renaissance of Enzyme Filamentation A Review By Chad K. Park & Nancy C. Horton Department of Molecular and Cellular Biology University of Arizona Tucson, AZ 85721 N. C. Horton ([email protected], ORCID: 0000-0003-2710-8284) C. K. Park ([email protected], ORCID: 0000-0003-1089-9091) Keywords: Enzyme, Regulation, DNA binding, Nuclease, Run-On Oligomerization, self-association 1 Abstract Filament formation by non-cytoskeletal enzymes has been known for decades, yet only relatively recently has its wide-spread role in enzyme regulation and biology come to be appreciated. This comprehensive review summarizes what is known for each enzyme confirmed to form filamentous structures in vitro, and for the many that are known only to form large self-assemblies within cells. For some enzymes, studies describing both the in vitro filamentous structures and cellular self-assembly formation are also known and described. Special attention is paid to the detailed structures of each type of enzyme filament, as well as the roles the structures play in enzyme regulation and in biology. Where it is known or hypothesized, the advantages conferred by enzyme filamentation are reviewed. Finally, the similarities, differences, and comparison to the SgrAI system are also highlighted. 2 Contents INTRODUCTION…………………………………………………………..4 STRUCTURALLY CHARACTERIZED ENZYME FILAMENTS…….5 Acetyl CoA Carboxylase (ACC)……………………………………………………………………5 Phosphofructokinase (PFK)……………………………………………………………………….6
    [Show full text]